Variant report

Variant	rs2572011
Chromosome Location	chr7:99487071-99487072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99485783..99488764-chr7:99489956..99491818,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10235630	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1025576	0.89[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1048705	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10808114	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1121592	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13310903	0.85[ASN][1000 genomes]
rs1865472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2060452	0.81[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2082744	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2082745	0.82[ASN][1000 genomes]
rs2099445	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2099446	0.91[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2247761	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2247762	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527881	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527899	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2527900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527901	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2527902	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527903	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2527904	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527906	0.94[ASN][1000 genomes]
rs2527907	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2527908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527909	0.94[ASN][1000 genomes]
rs2527911	0.96[ASN][1000 genomes]
rs2527912	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527913	0.96[ASN][1000 genomes]
rs2527914	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527915	0.96[ASN][1000 genomes]
rs2527916	0.97[ASN][1000 genomes]
rs2527918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527919	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527920	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527921	0.96[ASN][1000 genomes]
rs2527922	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527925	0.82[ASN][1000 genomes]
rs2527926	0.94[ASN][1000 genomes]
rs2527927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571991	0.88[ASN][1000 genomes]
rs2571992	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2571993	0.94[ASN][1000 genomes]
rs2571994	0.94[ASN][1000 genomes]
rs2571995	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571996	0.94[ASN][1000 genomes]
rs2571997	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2571998	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2571999	0.96[ASN][1000 genomes]
rs2572000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572002	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2572003	0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572005	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572006	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572008	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2572009	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2572010	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2572012	0.94[ASN][1000 genomes]
rs2572013	0.93[ASN][1000 genomes]
rs2572015	0.82[ASN][1000 genomes]
rs2572018	0.82[ASN][1000 genomes]
rs2572019	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2572022	0.82[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs2572023	0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs2572024	0.81[ASN][1000 genomes]
rs4727439	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474229	0.82[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7781442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809747	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	esv1792388	chr7:99468155-99497338	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv966726	chr7:99473527-99488698	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
6	esv3401805	chr7:99484666-99487814	ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2572011	TRIM4	cis	multi-tissue	Pritchard
rs2572011	TRIM4	cis	uninvolved skin	skin_eQTL
rs2572011	TRIM4	cis	Artery Tibial	GTEx
rs2572011	TRIM4	cis	lesional skin	skin_eQTL
rs2572011	OR2AE1	cis	cerebellum	SCAN
rs2572011	ORAI2	cis	parietal	SCAN
rs2572011	PILRB	cis	parietal	SCAN
rs2572011	OR2AE1	cis	parietal	SCAN
rs2572011	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2572011	TRIM4	cis	normal skin	skin_eQTL
rs2572011	PILRB	cis	multi-tissue	Pritchard
rs2572011	TRIM4	cis	Thyroid	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99458200-99489600	Weak transcription	Pancreas	Pancrea
2	chr7:99468400-99487200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:99470000-99489600	Weak transcription	Gastric	stomach
4	chr7:99472400-99487200	Weak transcription	Brain Anterior Caudate	brain
5	chr7:99472400-99487400	Weak transcription	Aorta	Aorta
6	chr7:99472600-99487200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:99472600-99487600	Weak transcription	Lung	lung
8	chr7:99472600-99488800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:99473000-99487200	Weak transcription	Brain Substantia Nigra	brain
10	chr7:99473200-99487200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:99479200-99488800	Weak transcription	Thymus	Thymus
12	chr7:99479800-99499200	Weak transcription	Small Intestine	intestine
13	chr7:99480400-99487800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:99480800-99487200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:99482600-99487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:99483000-99487200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr7:99484000-99487200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:99484600-99487200	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:99484600-99487200	Weak transcription	Spleen	Spleen
20	chr7:99484800-99487200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:99484800-99487200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:99485000-99487400	Weak transcription	Brain Angular Gyrus	brain
23	chr7:99485200-99487200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:99485200-99499000	Weak transcription	Psoas Muscle	Psoas
25	chr7:99485400-99487200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:99485400-99487200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:99485400-99487600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:99485400-99487800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:99485400-99489000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:99485600-99487200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:99485600-99487200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:99485600-99487200	Weak transcription	Ovary	ovary
33	chr7:99485600-99487200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:99485600-99487400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr7:99485600-99498200	Weak transcription	NHDF-Ad	bronchial
36	chr7:99485800-99487400	Weak transcription	Left Ventricle	heart
37	chr7:99485800-99487600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:99485800-99488000	Weak transcription	Fetal Heart	heart
39	chr7:99485800-99488800	Weak transcription	A549	lung
40	chr7:99485800-99489200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:99485800-99495400	Weak transcription	GM12878-XiMat	blood
42	chr7:99485800-99498200	Weak transcription	HSMMtube	muscle
43	chr7:99485800-99498800	Weak transcription	K562	blood
44	chr7:99486000-99487200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:99486000-99487600	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:99486000-99488000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:99486000-99488600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:99486000-99489600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:99486000-99497400	Weak transcription	Esophagus	oesophagus
50	chr7:99486200-99487200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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